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Make respiration differentiable/vectorized #74

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2 changes: 2 additions & 0 deletions docs/api_reference.md
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Expand Up @@ -16,6 +16,8 @@ hide:

::: diffwofost.physical_models.crop.partitioning.DVS_Partitioning

::: diffwofost.physical_models.crop.respiration.WOFOST_Maintenance_Respiration

## **Utility (under development)**

::: diffwofost.physical_models.config.Configuration
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160 changes: 160 additions & 0 deletions src/diffwofost/physical_models/crop/respiration.py
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"""Maintenance respiration for the WOFOST crop model."""

import datetime
import torch
from pcse.base import ParamTemplate
from pcse.base import RatesTemplate
from pcse.base import SimulationObject
from pcse.base.parameter_providers import ParameterProvider
from pcse.base.variablekiosk import VariableKiosk
from pcse.base.weather import WeatherDataContainer
from pcse.decorators import prepare_rates
from pcse.traitlets import Any
from diffwofost.physical_models.config import ComputeConfig
from diffwofost.physical_models.utils import AfgenTrait
from diffwofost.physical_models.utils import _broadcast_to
from diffwofost.physical_models.utils import _get_drv
from diffwofost.physical_models.utils import _get_params_shape


class WOFOST_Maintenance_Respiration(SimulationObject):
"""Maintenance respiration in WOFOST.

WOFOST calculates the maintenance respiration as proportional to the dry
weights of the plant organs to be maintained, where each plant organ can be
assigned a different maintenance coefficient. Multiplying organ weight
with the maintenance coeffients yields the relative maintenance respiration
(`RMRES`) which is than corrected for senescence (parameter `RFSETB`). Finally,
the actual maintenance respiration rate is calculated using the daily mean
temperature, assuming a relative increase for each 10 degrees increase
in temperature as defined by `Q10`.

**Simulation parameters** (provide in cropdata dictionary)

| Name | Description | Type | Unit |
|--------|---------------------------------------------------------- |------|------------------|
| Q10 | Relative increase in maintenance respiration rate with | SCr | - |
| | each 10 degrees increase in temperature | | - |
| RMR | Relative maintenance respiration rate for roots | SCr | kg CH₂O kg⁻¹ d⁻¹ |
| RMS | Relative maintenance respiration rate for stems | SCr | kg CH₂O kg⁻¹ d⁻¹ |
| RML | Relative maintenance respiration rate for leaves | SCr | kg CH₂O kg⁻¹ d⁻¹ |
| RMO | Relative maintenance respiration rate for storage organs | SCr | kg CH₂O kg⁻¹ d⁻¹ |
| RFSETB | Reduction factor for senescence | TCr | - |

**Rate variables**

| Name | Description | Pbl | Unit |
|-------|--------------------------------------------|----|-------------------|
| PMRES | Potential maintenance respiration rate | N | kg CH₂O ha⁻¹ d⁻¹ |

**Signals send or handled**

None

**External dependencies**

| Name | Description | Provided by | Unit |
|------|-------------------------------------|--------------------------------|-----------|
| DVS | Crop development stage | DVS_Phenology | - |
| WRT | Dry weight of living roots | WOFOST_Root_Dynamics | kg ha⁻¹ |
| WST | Dry weight of living stems | WOFOST_Stem_Dynamics | kg ha⁻¹ |
| WLV | Dry weight of living leaves | WOFOST_Leaf_Dynamics | kg ha⁻¹ |
| WSO | Dry weight of living storage organs | WOFOST_Storage_Organ_Dynamics | kg ha⁻¹ |

**Outputs**

| Name | Description | Pbl | Unit |
|-------|--------------------------------------------|----|---------------------|
| PMRES | Potential maintenance respiration rate | N | kg CH₂O ha⁻¹ d⁻¹ |

**Gradient mapping (which parameters have a gradient):**

| Output | Parameters influencing it |
|--------|------------------------------------------|
| PMRES | Q10, RMR, RML, RMS, RMO, RFSETB |
"""

params_shape = None # Shape of the parameters tensors

@property
def device(self):
"""Get device from ComputeConfig."""
return ComputeConfig.get_device()

@property
def dtype(self):
"""Get dtype from ComputeConfig."""
return ComputeConfig.get_dtype()

class Parameters(ParamTemplate):
Q10 = Any()
RMR = Any()
RML = Any()
RMS = Any()
RMO = Any()
RFSETB = AfgenTrait()

class RateVariables(RatesTemplate):
PMRES = Any()

def __init__(self, kiosk, publish=None):
self.PMRES = torch.tensor(
0.0, dtype=ComputeConfig.get_dtype(), device=ComputeConfig.get_device()
)
super().__init__(kiosk, publish=publish)

def initialize(self, day: datetime.date, kiosk: VariableKiosk, parvalues: ParameterProvider):
"""Initialize the maintenance respiration module.

Args:
day: Start date of the simulation
kiosk: Variable kiosk of this PCSE instance
parvalues: ParameterProvider object providing parameters as key/value pairs
"""
self.params = self.Parameters(parvalues)
self.rates = self.RateVariables(kiosk, publish=["PMRES"])
self.kiosk = kiosk
self.params_shape = _get_params_shape(self.params)

@prepare_rates
def calc_rates(self, day: datetime.date, drv: WeatherDataContainer):
"""Calculate maintenance respiration rates.

Args:
day: Current date
drv: Weather data for the current day
"""
p = self.params
kk = self.kiosk
r = self.rates

Q10 = _broadcast_to(p.Q10, self.params_shape, dtype=self.dtype, device=self.device)
RMR = _broadcast_to(p.RMR, self.params_shape, dtype=self.dtype, device=self.device)
RML = _broadcast_to(p.RML, self.params_shape, dtype=self.dtype, device=self.device)
RMS = _broadcast_to(p.RMS, self.params_shape, dtype=self.dtype, device=self.device)
RMO = _broadcast_to(p.RMO, self.params_shape, dtype=self.dtype, device=self.device)

WRT = _broadcast_to(kk["WRT"], self.params_shape, dtype=self.dtype, device=self.device)
WLV = _broadcast_to(kk["WLV"], self.params_shape, dtype=self.dtype, device=self.device)
WST = _broadcast_to(kk["WST"], self.params_shape, dtype=self.dtype, device=self.device)
WSO = _broadcast_to(kk["WSO"], self.params_shape, dtype=self.dtype, device=self.device)
DVS = _broadcast_to(kk["DVS"], self.params_shape, dtype=self.dtype, device=self.device)

TEMP = _get_drv(drv.TEMP, self.params_shape, dtype=self.dtype, device=self.device)

RMRES = RMR * WRT + RML * WLV + RMS * WST + RMO * WSO
RMRES = RMRES * p.RFSETB(DVS)
TEFF = Q10 ** ((TEMP - 25.0) / 10.0)
PMRES = RMRES * TEFF

# No maintenance respiration before emergence (DVS < 0).
r.PMRES = torch.where(DVS < 0, torch.zeros_like(PMRES), PMRES)

def __call__(self, day: datetime.date, drv: WeatherDataContainer):
"""Calculate and return maintenance respiration (PMRES)."""
self.calc_rates(day, drv)
return self.rates.PMRES

def integrate(self, day: datetime.date, delt: float = 1.0):
"""No state variables to integrate for this module."""
return
1 change: 1 addition & 0 deletions tests/physical_models/conftest.py
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Expand Up @@ -14,6 +14,7 @@
"phenology",
"partitioning",
"assimilation",
"respiration",
]
FILE_NAMES = [
f"test_{model_name}_wofost72_{i:02d}.yaml" for model_name in model_names for i in range(1, 45)
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